Phylogenetic trees were used to visualize metabolic differences between taxa, and were constructed using the GToTree pipeline [1]} with the “universal” protein set defined by Hug et al. [2]}.
GToTree identifies target genes with HMMER3 [3]}, aligns them with MUSCLE [4]}, and trims alignments with trimAl [5]}. Trees were generated from the aligned and concatenated gene sets using FastTree [6]}, and visualized using iToL [7]}.
